"The reasons are once again incorrect reports concerning the payment of wages and social security deductions," said a statement on the SFV website.
It added that the problem, reported by the Swiss league's licensing committee, concerned the payments for November.
Neuchatel have suffered two four-point deductions and Swiss media have reported that a further penalty could result in the club being expelled from the country's Super League, which is on its winter break and restarts on February 4.
The Swiss Players' Union complained this month that the Neuchatel squad were owed two months' wages and described the situation as "unacceptable".
Neuchatel owner Bulat Chagaev (pictured), a businessman who hails from the volatile region of Chechnya, bought the club in May saying that he wanted to take Neuchatel into the Champions League.
Chagaev has since sacked four coaches and faced a boycott by fans. He also fired the club's administrative staff last year and ended all the sponsorship contracts.
In November, Neuchatel survived a request for bankruptcy made by a players' agent who took the club to court alleging that he was owed 400,000 Swiss francs.
However, public prosecutors have since opened another case alleging that Chagaev had falsified a letter from a bank he used during a hearing.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.